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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gwascat_2.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gwascat.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.39.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gwascat’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 34.0Mb
  sub-directories of 1Mb or more:
    data     10.1Mb
    legacy   15.6Mb
    obo       3.0Mb
    olddata   2.2Mb
    tab       1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindcadd_snv: no visible global function definition for ‘TabixFile’
bindcadd_snv: no visible global function definition for ‘findOverlaps’
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘snpsBySeqname’
gwascat_from_AHub: no visible binding for global variable ‘si.hs.38’
gwcat_snapshot: no visible binding for global variable ‘si.hs.38’
lo38to19: no visible global function definition for ‘liftOver’
lo38to19: no visible binding for global variable ‘si.hs.37’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
process_gwas_dataframe: no visible binding for global variable
  ‘si.hs.38’
snpGenos: no visible global function definition for ‘getSNPlocs’
tfilt: no visible binding for global variable ‘phr’
tpad: no visible binding for global variable ‘phr’
traitsManh: no visible global function definition for ‘aes’
traitsManh: no visible binding for global variable ‘PVALUE_MLOG’
variantProps: no visible binding for global variable ‘gwrngs’
Undefined global functions or variables:
  PVALUE_MLOG TabixFile aes findOverlaps getSNPlocs gwrngs gwrngs19
  liftOver phr si.hs.37 si.hs.38 snpsBySeqname
* checking Rd files ... NOTE
checkRd: (-1) gwcex2gviz.Rd:33: Escaped LaTeX specials: \_
checkRd: (-1) traitsManh.Rd:18: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 79887 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 R_LIBS=/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoRgwRp/RLIBS_f9a51cc72f7e R_ENVIRON_USER='' R_LIBS_USER='NULL' R_LIBS_SITE='NULL' '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'gwascat-Ex.Rout' 2>&1 < 'gwascat-Ex.R'
 ERROR
Running examples in ‘gwascat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ldtagr
> ### Title: expand a list of variants by including those in a VCF with LD
> ###   exceeding some threshold; uses snpStats ld()
> ### Aliases: ldtagr
> ### Keywords: models
> 
> ### ** Examples
> 
>  cand = GenomicRanges::GRanges("1", IRanges::IRanges(113038694, width=1))
>  names(cand) = "rs883593"
>  requireNamespace("VariantAnnotation")
>  expath = dir(system.file("vcf", package="gwascat"), patt=".*exon.*gz$", full=TRUE)
>  tf = Rsamtools::TabixFile(expath)
>  ldtagr( cand, tf, lbR2 = .8)

 *** caught segfault ***
address 0x1, cause 'invalid permissions'

Traceback:
 1: snpStats::ld(gt[, snpid], gt, stats = "R.squared")
 2: ldtagr(cand, tf, lbR2 = 0.8)
An irrecoverable exception occurred. R is aborting now ...
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gwascat_from_AHub 9.464  0.245  10.368
gwcat_snapshot    8.565  0.238   9.065
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/gwascat.Rcheck/00check.log’
for details.